Before the end of the movie we saw Kouzuki did posses different body parts inside jars in his basement. It's a possibility that he had chopped her into pieces after she hang herself and showed it to Hideko. In other words, if she tried to run she would suffer the same fate. That might be a possible answer for how the uncle killed her aunt. The aunt killed herself clearly visible in the movie but it is a possibility that the uncle chopped her dead body into pieces.
One of the reasons for her suicide might be an encounter with the octopuss that is also in the cellar. The uncle had books with images of women having sexual intercourse with this animal so maybe the aunt had also alife or dead in front of Hideko.
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